When carbon dioxide is introduced into the subsurface it will migrate upwards and can encounter faults, which, depending on their hydrogeological properties and composition, can form barriers or pathways for the migrating fluid. We analyse uncertainties associated with these properties in order to better understand the implications for the retention of CO₂ in the subsurface. We show that faults that form seals for other fluids may not be seals for CO₂, which has implications for storage sites.